You can use the fsck subcommand to check for problems in your data. What
can be checked depends on the key-value backend you've used
for the data. For example, when you use the SHA1 backend, fsck will verify
that the checksums of your files are good. Fsck also checks that the
numcopies setting is satisfied for all files.

Use -S or --incremental to start the incremental check. Use -m
or --more to continue the started check and continue where it left
off. Note that saving the progress of fsck is performed after every
1000 files or 5 minutes or when --time-limit occours. There may be
files that will be checked again when git-annex exists abnormally
eg. Ctrl+C and the check is restarted.